Background Roux-en-Y (R-Y) gastric bypass, also known as bariatric surgery, sometimes causes postoperative hyperoxaluria and subsequent oxalate nephrolithiasis in obese patients. In this study, we retrospectively investigated the frequency of occurrence of nephrolithiasis and renal dysfunction in postoperative gastric cancer patients with respect to the surgical procedures employed. Methods Two hundred and twenty-six consecutive gastric cancer patients, who underwent distal gastrectomy with Billroth-I reconstruction (DGBI, 60 patients), distal gastrectomy with R-Y reconstruction (DGRY, 81 patients), and total gastrectomy with R-Y reconstruction (TGRY, 85 patients), were investigated for postoperative nephrolithiasis and renal dysfunction. We also examined the risk factors for postoperative nephrolithiasis in these patients with gastric cancer. Results Nephrolithiasis was detected in 3 (5 %), 7 (9 %), and 21 (25 %) patients in the DGBI, DGRY, and TGRY groups, respectively. There were significant differences in the frequency of nephrolithiasis between the DGBI and TGRY groups (p = 0.004), and between the DGRY and TGRY groups (p = 0.011), but there was no significant difference between the DGBI and DGRY groups. Multivariate logistic regression analysis revealed that gender and extent of gastrectomy were independent risk factors associated with nephrolithiasis. Renal dysfunction was found in 5 patients (6 %) in the TGRY group, but was not found in either the DGBI or the DGRY group. Nephrolithiasis was detected in all these 5 patients, and a renal biopsy performed in one patient revealed the presence of intratubular calcium oxalate crystals with chronic tubulointerstitial nephritis. Conclusion Total gastrectomy with R-Y reconstruction was an independent predictive factor for nephrolithiasis in patients with gastric cancer.